The gastrointestinal epithelium comprises the primary cellular barrier against omnipresent luminal antigens, and actively participates as an innate immune sensor of microbial pathogens and commensal organisms. As such, intestinal epithelia define the central interface for host-microbiota interactions and intestinal homeostasis. Based on their juxtaposition to the anoxic gut lumen, intestinal epithelial cells function physiologicall in a low- oxygen-tension microenvironment, and exhibit a uniquely adaptive oxygenation profile. In active inflammation associated with inflammatory bowel disease (IBD), mucosal metabolism is profoundly altered, resulting in nutrient and oxygen depletion or hypoxia. Adaptive transcriptional programs elicited by oxygen deprivation in mammalian cells are mediated primarily through the hypoxia-inducible factor (HIF) complex. A protective role for HIF in orchestrating epithelial gene regulation has been identified, with transcriptional responses integrated to specifically support barrier function and adaptations to the hypoxic microenvironment. Genome-wide profiling of HIF target loci highlighted two novel hypoxia-regulated pathways implicated in the host-microbial metabolic axis: the creatine kinase shuttle that promotes spatiotemporal ATP buffering and barrier energetics, and selective autophagy. Autophagy, a highly conserved catabolic pathway, coordinates diverse aspects of cellular and organismal responses to metabolic stressors and infection and has recently been ascribed a key role in the elimination of invasive bacteria (xenophagy). Importantly, epithelial autophagic pathways are dysregulated in IBD. While significant efforts have focused on identification of core autophagy components, regulation of epithelial autophagy at the transcriptional level is poorly characterized. In particular, little is known regarding the coordination of canonical autophagy gene responses and how these modulate xenophagic capture of intracellular pathogens. A fundamental link between selective autophagy of damaged mitochondria (mitophagy) and infectious disease has recently been established, and mitochondrial energetics have been shown to significantly influence the clinical course of murine colitis. Our ongoing studies have identified a cohort of both mitophagic (BNIP3L) and xenophagic (NOD2) genes that are induced by hypoxia and HIF- stabilization in epithelia. Preliminary work has revealed that invasive bacteria are effectively targeted by xenophagy under hypoxic conditions in a HIF-dependent manner. Epithelial HIF-deficient mice demonstrate increased bacterial dissemination and disease activity following acute bacterial challenge. Moreover, augmentation of HIF-mediated creatine metabolism and epithelial bioenergetics proved protective in mouse models of intestinal inflammation. Based on these observations, we hypothesize that epithelial HIF pathways converge in a cell autonomous manner to coordinate mitochondrial and metabolic homeostasis with invasive microbe detection.